---
name: "MindTheGap"
section: "1"
platform: "linux"
package: "mindthegap"
version: "2.3.0-2"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/MindTheGap"
---

# MindTheGap(1)

Perform detection and assembly of DNA insertion variants

## NAME

MindTheGap - Perform detection and assembly of DNA insertion variants

## SYNOPSIS

**MindTheGap** \<module\> \[module options\]

## DESCRIPTION

MindTheGap is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detected insertion sites, the other is the set of assembled insertions for each breakpoint.

MindTheGap can also be used as a genome assembly finishing tool: it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file.\
\
find - insertion breakpoint detection. \
 Usage: **MindTheGap** find ( -in  *\<reads.fq\>* \| -graph *\<graph.h5\>* ) -ref *\<reference.fa\>* \[option\]\
\
fill - gap-filler or insertion assembly\
 Usage: **MindTheGap** fill ( -in  *\<reads.fq\>* \| -graph *\<graph.h5\>* ) ( -bkpt  *\<breakpoints.fa\>* \| -contig *\<contig.fa\>* ) \[options\]

## COMMON OPTIONS

help - display the MindTheGap help menu\
 Usage: **MindTheGap** -help\
\
version - display current version\
 Usage: **MindTheGap** -version